Decoupled evolution of antimicrobial repertoires in lichen-forming fungi

Abstract

Lichens are stable multipartite symbioses in which a fungal mycobiont associates with one or more photosynthetic partners while hosting complex microbiomes. Secreted antimicrobial proteins (AMPs) have recently emerged as important mediators of fungal interactions with surrounding microbial communities, yet their evolutionary distribution and diversity in lichen-forming fungi remain largely unexplored. Here, we predicted AMP repertoires across 80 phylogenetically diverse lichen-forming fungi representing three photobiont association types. Contrary to our expectation, average repertoire size did not differ between chlorolichens, cyanolichens and tripartite lichens (363 AMPs per species overall), even though repertoire size varied almost five-fold among species and 23 AMP families showed photobiont-associated enrichment or depletion. This quantitative conservation masks extensive compositional turnover, with families occurring in at least 90% of species coexisting alongside numerous lineage-specific groups. Pooled population sequencing of 11 Umbilicaria phaea populations along two elevational gradients further revealed recurrent AMP presence– absence variation within a single species. In contrast to AMPs, biosynthetic gene clusters (BGCs) and carbohydrate-active enzymes (CAZymes), which include known antimicrobials, were markedly reduced in cyanolichens relative to chlorolichens. Lichen-forming fungi thus combine a conserved baseline antimicrobial protein capacity, whose composition nonetheless turns over between lineages and populations, with chemical and enzymatic systems that differentiate along photobiont association and may support ecological and lifestyle-associated adaptation. SIGNIFICANCE STATEMENT Lichen-forming fungi interact simultaneously with photosynthetic partners and diverse microbial communities, yet how their antimicrobial capacity evolves in this complex symbiotic context is poorly understood. By comparing 80 lichen-forming fungal genomes, we show that the size of their predicted antimicrobial protein repertoires is broadly conserved across associations with green algae, cyanobacteria, or both, despite extensive turnover in the constituent protein families across lineages and populations. In contrast, carbohydrate-active enzymes and biosynthetic gene clusters vary substantially with photobiont association. These findings reveal a decoupling of antimicrobial repertoire size from repertoire composition and from other antimicrobial molecules, suggesting that distinct molecular repertoires are subject to different evolutionary constraints. Thus, lichen-forming fungi maintain a broadly conserved genomic potential for protein-based antimicrobial activity while retaining substantial molecular flexibility.